The properties of nanocomposites are directly affected by the filler–matrix interaction and therefore surface filler modification is often necessary to improve the mechanical properties of nanocomposites. Our study evaluated surface modification of sepiolite (SEP) on properties of poly(butylene adipate‐co‐terephthalate) (PBAT)‐based nanocomposites. The nanofillers were modified using two organic modifiers, octadecyl isocyanate (OI), and 3‐aminopropyltriethoxysilane (APTES). OI showed higher treatment efficiency than APTES and better results in alkyl groups on the surface of the nanofiller, with crystalline profile, which remained in the nanocomposites. The effect of organo‐sepiolites on the properties of PBAT nanocomposites was investigated by DSC, XRD, TGA, FTIR, scanning electron microscopy (SEM), and mechanical tensile tests. TGA analysis showed that the addition of O‐SEP on PBAT decreases its thermal stability. SEM analysis showed cavities and fiber tips in the matrix associated with clay agglomerates and some untreated clay faces, which impair filler‐matrix interfacial adhesion. Both treatments increased the elastic modulus and preserved the elongation and tensile strength of PBAT and the treatment with OI results in a higher modulus. Although some studies to improve the clay dispersion are necessary, the promising results reveal the potential of using OI and APTES as SEP modifiers to reinforce PBAT or other polyesters.